The only legal maneuver remaining was an appeal to the Supreme Court of the United States, then presided over by Chief Justice Morrison R. Waite, for another Writ of Error. To bolster its legal expertise and influence, the defense committee hired three new attorneys to assist Captain Black. These were Roger Pryor, a former congressman from Virginia who had fought for the Confederacy but moved to New York after the war and established a very successful legal practice; John Randolph Tucker, another Virginian, who was elected to Congress in 1874 and afterward had become a professor of constitutional law and then dean at Washington and Lee law school; and Benjamin Butler, the often controversial Union officer, Massachusetts congressman and governor, and 1884 Greenback-Labor candidate for president.

Writing to Captain Black after the executions, Butler likened the treatment of the Haymarket defendants to the "judicial murders" (a term the anarchists often used to describe what was happening to them) resulting from the trials in his own state two centuries earlier of alleged witches, whom he called "the Anarchists of that day."

The delegation of five defense lawyers (Moses Salomon still assisted Black) appeared on October 21, 1887, before Associate Justice John M. Harlan, who suggested that that the application be made before the entire court immediately. This decision was made to save time when "human life and liberty" were hanging in the balance, since, if Harlan approved the application, the whole court would hear the case anyway, and, if he did not, the attorneys would then approach another justice.

Pryor made his presentation to the whole court early in the afternoon. On October 24, Chief Justice Waite stated that the Court would hold a hearing on whether a Writ of Error should be issued. He made it clear, however, that he and his brethren would not intervene unless "federal questions were actually made and decided in the Supreme Court of the State," and in a way "such as to make it proper for us to bring the case here for review." In other words, unless federal law was involved in some significant way that superseded the state's jurisdiction, a federal tribunal could not issue a writ.

The lawyers for the anarchists and the state made their presentations in the tense and crowded court on October 27 and 28. The attorneys for the defense challenged the Illinois statute regarding the impanelment of juries "on the ground of repugnancy to the Constitution of the United States." They cited the fourth, fifth, sixth, and fourteenth amendments to the Constitution in claiming that their clients' prosecution involved unlawful search and seizure, involuntary self-incrimination, a prejudiced jury, and the denial of due process and equal protection of the laws by the state of Illinois. Illinois State's Attorney Grinnell and Attorney General Hunt countered that no federal question was involved.

On November 2, Waite spoke for the entire court in dismissing the application. He stated that for more than a half century the Supreme Court had adhered to the view that the first ten amendments to the Constitution "were not intended to limit the powers of the state government in respect to their own people, but to operate on the National Government alone." As to the fourteenth amendment, which limited the state's power to abridge a citizen's rights without due process, neither Illinois law nor the conduct of the case had done this.

To the extent that the defense might have had a case in regard to the use of illegally seized correspondence between the infamous anarchist Johann Most and defendant Adolph Spies, defense attorneys had no basis for appeal since they did not raise an objection on this point at the trial itself. The issue of whether Spies's testimony involved improper questioning that forced him to incriminate himself was a matter of state and not federal law. Regarding the jury selection, Waite said that there was no "manifest error" in the trial court's judgment that the members of this body were sufficiently impartial to hear the case. Waite similarly judged other smaller points insufficient to justify the writ.

Waite (1816-1888) had been appointed Chief Justice by President Ulysses S. Grant in 1874, and during his tenure the Supreme Court made numerous decisions that supported the claims of states' rights advocates, even when these claims severely weakened the rights of recently freed slaves. He and the other justices may have been hesitant to interfere in what they saw as a state matter. William Salter of the Chicago Ethical Culture Society, one of the leading critics of the trial, reported that he received a letter from Associate Justice Samuel F. Miller explaining that the meaning of the dismissal was not that the justices found the men innocent or guilty, but that the state had conducted a legal trial. On the other hand, he and the other justices may have been caught up in public mood, which still overwhelmingly favored the verdict.

On November 4, the Chicago Tribune carried the story that a mysterious package containing glass tubing, wires, percussion caps, and an explosive charge was delivered to Chief Justice Waite's home. He and his wife "handled the contrivance fearlessly and examined it with curiosity," deeming it a hoax, but the police were investigating the matter.